Course: Comparative Genomics: from evolution to function


June 27 – July 1 2011, Utrecht


  • dr. Berend Snel
  • prof. dr. Martijn Huynen
  • prof. dr. Jaap Heringa
  • Contact: dr. Berend Snel, e-mail:


Utrecht University, Kruyt Building Paduaan 8 3584 CH Utrecht

Target audience

The course is intended for PhD students and master students in bioinformatics, especially those interested in evolution and/or those who want to compare various genomics data between species.Participants are expected to have some hands on experience with blast, constructing multiple sequence alignments and phylogenetic trees, and in addition to have some familiarity with concepts such as orthology, synteny and protein domains.


Genomics data give a comprehensive, but one dimensional and often rather noise image of the cell. Comparative genomics between species and between types of data facilitates the understanding of what these data really reflect about the underlying processes. Comparative genomics therewith relies on a solid understanding of basic elements of Bioinformatics like homology, orthology and similarities arising by chance. Moreover it is important to know the assumptions andheuristics of bioinformatic methods for comparative genomics and hence we aim to let participants develop an understanding of why they fail (or misdetect) as a consequence of a variety of biological /evolutionary causes.

The first two days of the course provide a basis for the course with the aim to move “beyond blast” in terms of more sensitive homology searches, domain level analysis of protein evolution as well as morefine grained definitions of relatedness as can be obtained from the proper interpretation of gene trees (i.e. various levels of orthology).This foundation is used to discuss in the three following days in more detail three topics: (1) the study of  functional and evolutionary consequence of (genome) duplications, (2) the evolution of interactions and complexes and (3) the prediction and evolution of genomic regulatory elements.

Concept course schedule

Day 1 Distant homology and protein domains (lecturer Jaap Heringa)

Topics & Tools: hhsearch, psiblast, pfam, homology and function, undetected orthology from failure to detect homology

Day 2 Small scale orthology and large scale databases (lecturers Martijn Huynen, Berend Snel)

Topics & Tools: tree reconciliation, relation between homology and orthology, ensembl compara, COGs, inparalogs vs outparalogs, fusion and fission

Day 3 Genome duplications (lecturer Berend Snel)

Topics & Tools: yeast gene order browser, synteny, consequences of genome duplications, timing of duplications, ensembl biomart

Day 4 Comparative Interactomics (lecturers Jaap Heringa, Berend Snel)

Topics & Tools: network alignment, phylogenetic profiles, biogrid, cytoscape, neofunctionalization vs subfunctionalization

Day 5 Prediction and Evolution of Gene Regulation  (lecturer Martijn Huynen)

Topics & Tools: chip-seq, phylogenetic footprinting, gibbs sampling

Registration and course fee

You can register for this course by filling out the online registration form.

The maximum number of participants is 20 so register soon to be sure of a course seat! Information about the course fee can be found at the enrolment page.

The fee includes:

  • Course material: Handouts and papers to be discussed will be handed out at the start of the course. Software required for the lab course will be made available online.
  • Catering: Coffee, tea and soft drinks and lunch will be provided.
  • Drinks will be organized in the afternoon of Tuesday June 28 in conjunction with the RSG Netherlands.

For more information about the course programme you can contact Celia van Gelder.

For more information about the registration or logistics you can contact NBIC office.